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polish: make genes read by list instead of ls

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kuoi 2024-07-03 10:54:01 +10:00
parent 7636c65c5a
commit 3a761cbe2a
1 changed files with 28 additions and 8 deletions
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36
batch.sh
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@ -21,7 +21,7 @@ HELP=false
### Get some arrays ### Get some arrays
ARGS=$(getopt -o c:,f:,h,l:,m:,r:,t: --long contig:,functions:,help,list:,memory:,reference:,threads: -n 'batch.sh' -- "$@") ARGS=$(getopt -o c:,f:,g:,h,l:,m:,r:,t: --long contigs:,genes:,functions:,help,list:,memory:,reference:,threads: -n 'batch.sh' -- "$@")
if [ $? != 0 ]; then if [ $? != 0 ]; then
echo "Failed to parse options." >&2 echo "Failed to parse options." >&2
exit 1 exit 1
@ -30,11 +30,16 @@ eval set -- "$ARGS"
while true; do while true; do
case "$1" in case "$1" in
-c|--contig) -c|--contigs)
case "$2" in case "$2" in
"") ARG_C='scaffolds'; shift 2 ;; "") ARG_C='scaffolds'; shift 2 ;;
*) ARG_C=$2; shift 2 ;; *) ARG_C=$2; shift 2 ;;
esac ;; esac ;;
-g|--genes)
case "$2" in
"") shift 2 ;;
*) ARG_G=$2; shift 2 ;;
esac ;;
-f|--functions) -f|--functions)
case "$2" in case "$2" in
"") ARG_F='all'; shift 2 ;; "") ARG_F='all'; shift 2 ;;
@ -45,14 +50,15 @@ while true; do
Version: $pkgver\n \ Version: $pkgver\n \
License: GPL-3.0-only\n \ License: GPL-3.0-only\n \
Author: Guoyi Zhang\n \ Author: Guoyi Zhang\n \
-c\t--contig\tcontings type: scaffolds or contigs\n \ -c\t--contigs\tcontings type: scaffolds or contigs\n \
-g\t--genes\tgene file path\n \
-f\t--functions\tfunctions type (optional): all clean assembly fasta map pre split merge align\n \ -f\t--functions\tfunctions type (optional): all clean assembly fasta map pre split merge align\n \
-h\t--help\thelp: show this information\n \ -h\t--help\thelp: show this information\n \
-l\t--list\tlist file path\n \ -l\t--list\tlist file path\n \
-m\t--memory\tmemory settings (optional, default 16 GB)\n \ -m\t--memory\tmemory settings (optional, default 16 GB)\n \
-r\t--reference\treference genome path\n \ -r\t--reference\treference genome path\n \
-t\t--threads\tthreads setting (optional, default 8 threads)\n \ -t\t--threads\tthreads setting (optional, default 8 threads)\n \
for example: bash $0 -c scaffolds -f all -l list -r Reference.exons.aa.fas \n" for example: bash $0 -c scaffolds -f all -l list -g genes -r Reference.exons.aa.fas \n"
HELP=true HELP=true
shift ;; shift ;;
-l|--list) -l|--list)
@ -89,7 +95,9 @@ if [ "$HELP" = false ]; then
fi fi
readarray -t full_names < "$ARG_L" readarray -t full_names < "$ARG_L"
readarray -t genes < "$ARG_G"
length_fn=${#full_names[@]} length_fn=${#full_names[@]}
length_gn=${#genes[@]}
fi fi
### Quality control && Trimming ### Quality control && Trimming
@ -214,12 +222,18 @@ fi
if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "merge" ]; then if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "merge" ]; then
## Check if the genes is specified
if [ -z "$ARG_G" ] ; then
echo "Argument of genes list missing."
exit 1
fi
mkdir -p $DirMerge mkdir -p $DirMerge
cd $DirSplit cd $DirSplit
for genes in $(ls) for (( i=0; i<$length_gn; i++ ))
do do
cd $genes cd ${genes[$i]}
cat * > ../$genes.fasta cat * > ../${genes[$i]}.fasta
cd .. cd ..
done done
mv *.fasta ../$DirMerge mv *.fasta ../$DirMerge
@ -229,10 +243,16 @@ fi
if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "align" ]; then if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "align" ]; then
## Check if the genes is specified
if [ -z "$ARG_G" ] ; then
echo "Argument of genes list missing."
exit 1
fi
mkdir -p $DirAlign mkdir -p $DirAlign
mkdir -p $DirAlign/AA && mkdir -p $DirAlign/NT mkdir -p $DirAlign/AA && mkdir -p $DirAlign/NT
cd $DirMerge cd $DirMerge
for genes in $(ls | sed "s@.fasta@@g") for (( i=0; i<$length_gn; i++ ))
do do
java -jar $PathMacse -prog alignSequences -seq ${genes}.fasta -out_AA ../$DirAlign/AA/$genes.fasta -out_NT ../$DirAlign/NT/$genes.fasta java -jar $PathMacse -prog alignSequences -seq ${genes}.fasta -out_AA ../$DirAlign/AA/$genes.fasta -out_NT ../$DirAlign/NT/$genes.fasta
done done